The input for the pipeline is a list of mapped read pairs and a list of restriction enzyme sites in the genome, and the output is a list of interacting fragment end pairs.
The pipeline itself is scell_hicpipe_core_1_2.tar.gz, and an example input dataset (for cell-5 in the above Nagano et al. paper) can be found in scell_hicpipe_test_project_1_0.tar.gz.